Bond fukui indices: Comparison of frozen molecular orbital and finite differences through mulliken populations

Bond Fukui functions and matrices are introduced for ab initio levels of theory using a Mulliken atoms in molecules model. It is shown how these indices may be obtained from first‐order density matrix derivatives without need for going to second‐order density matrices as in a previous work. The importance of taking into account the nonorthogonality of the basis in ab initio calculations is shown, contrasting the present results with previous work based on Hückel theory. It is shown how the extension of Fukui functions to Fukui matrices allows getting more insight into the nature of bond Fukui functions. All presently introduced indices respect the necessary normalization conditions and include the classical single atom condensed Fukui functions. © 2013 Wiley Periodicals, Inc.     

Asymptotic properties of the exchange energy density and the exchange potential of finite systems: relevance for generalized gradient approximations

It is shown that generalized gradient approximations (GGAs) for exchange only, due to their very limited form, quite generally can not simultaneously reproduce both the asymptotic forms of the exchange energy density and the exchange potential of finite systems. Furthermore, mechanisms making GGAs formally approach at least one of these asymptotic forms do not improve the corresponding quantity in the relevant part of the asymptotic regime of atoms. By constructing a GGA which leads to superior atomic exchange energies compared to all GGAs heretofore but does not reproduce the asymptotic form of the exact exchange energy density it is demonstrated that this property is not important for obtaining extremely accurate atomic exchange energies. We conclude that GGAs by their very concept are not suited to reproduce these asymptotic properties of finite systems. As a byproduct of our discussion we present a particularly simple and direct proof of the well known asymptotic structure of the exchange potential of finite spherical systems.     

Comparison between conventional indirect competitive enzyme-linked immunosorbent assay (icELISA) and simplified icELISA for small molecules

A simplified indirect competitive enzyme-linked immunosorbent assay (icELISA) for small molecules was established by modifying the procedure of conventional icELISA. The key change was that the analyte, antibody, and enzyme-labeled second antibody in the simplified icELISA were added in one step, whereas in conventional icELISA these reagents were added in two separate steps. Three small chemicals, namely zeatin riboside, glycyrrhetinic acid, and chlorimuron-ethyl, were used to verify the new assay format and compare the results obtained from conventional icELISA and simplified icELISA. The results indicated that, under optimized conditions, the new assay offered several advantages over the conventional icELISA, which are simpler, less time consuming and higher sensitive although it requires more amount of reagents. The assay sensitivity (IC₅₀) was improved for 1.2-1.4-fold. Four licorice roots samples were analyzed by conventional icELISA and simplified icELISA, as well as liquid chromatography (LC). There was no significant difference among the content obtained from the three methods for each sample. The correlation between data obtained from conventional icELISA and simplified icELISA analyses was 0.9888. The results suggest that the simplified icELISA be useful for high throughput screening of small molecules.     

Competition between reactivity and relaxation in free electron attachment to molecules

The reactivity of the C₆F₅X (X=F, Cl, Br, I) molecules following low energy (0–15 eV) electron attachment is studied in the gas phase under single collision conditions, free molecular clusters and condensed molecules by means of crossed beams and surface experiments. All four molecules exhibit a very prominent resonance for low energy electron attachment (<1 eV, attachment cross section >10⁻¹⁴ cm²). Under collision free conditions thermal electron capture generates long lived molecular parent anions C₆F₅X^−*. Along the line Cl, Br, I dissociation into X⁻+C₆F₅ and X+C₆F₅-increasingly competes until for X=1 only chemical fragmentation is observed on the mass spectrometric time scale. In free molecular clusters chemical fragmentation is quantitatively quenched at low energies in favour of associative attachment yielding undissociated, relaxed ions (C₆F₅X)⁻ _n,n≥1. A further dissociative resonance at 6.5 eV in C₆F₅Cl is considerably enhanched in clusters. If these molecules are finally condensed on a solid surface, one observes a prominent Cl⁻ desorption resonance at 6.5 eV. While the quantitative quenching of the chemical reactivity at low energies is due to the additional possibilities of energy dissipation under aggregation, the enhanched reactivity at 6.5 eV is interpreted by the conversion of a core excited open channel resonance in single molecules into a closed channel (Feshbach) resonance when it is coupled to environmental molecules.     

Analogies and differences between two ways to evaluate the global hardness

The weight of the energetic components (electronic kinetic, electron-nucleus and electron-electron Coulombic, and correlation energies) of the ionization potential, electron affinity, chemical potential, and global hardness is evaluated and contrasted with the energetic components of the hardness kernel and the experimental values of these properties for 40 systems. The contrast of the hardness terms obtained from finite difference and hardness kernel gives some insight on the possible implications to differentiate the electronic energy with respect to the number electrons or the electron density.     

Concurrent symmetries: the interplay between local and global molecular symmetries

We analyze in this article the degree to which different groups of atoms retain local symmetries when assembled in a molecule. This study is carried out by applying continuous symmetry measures to several families of mixed sandwiches, a variety of piano-stool molecules, and several organic groups. An analysis of the local symmetry of the electron density shows that, sandwiched between two regions of different symmetry that correspond to the ligand sets, its symmetry is cylindrical at the central metal atom.     

Recombination kinetics of molecules with anisotropic reactivity and interaction potential. Exact solution for a small reactive region

The Smoluchowski equation for a pair of molecules with anisotropic reactivity and interaction potential is solved in the limit of a small reactive region (small reactive patches). In the steady-state case steric factors are calculated using this solution. The kinetics of geminate pair recombination is also obtained and analyzed in detail.     

Koopmans-like approximation in the Kohn-Sham method and the impact of the frozen core approximation on the computation of the reactivity parameters of the density functional theory

A Koopmans-like approximation is introduced in the spin-polarized version of the Kohn-Sham (KS) density functional theory to obtain a relation between KS orbital energies and vertical ionization potential and electron affinity. Expressions for reactivity indexes (like electronegativity, hardness, electrophilicity, and excitation energies) include KS frontier orbital energies and additional contributions associated with the self-interaction correction. Those reactivity parameters were computed with different exchange-correlation functionals to test the approach for a set of small molecules. The results show that the present approximation provides a better way to estimate hardness, electronegativity, and electrophilicity than just the use of frontier orbital energy values. However KS HOMO and LUMO energy gap gives a better agreement with excitation energies.     

Establishment of correlations between the structure and reactivity of molecules in the gas phase based on information theory

A general approach to revealing correlations between the structure of molecules and their reactivity in fragmentation processes under electron impact conditions based on the use of generalized structural and mass spectral characteristics is suggested. The characteristics were obtained using information theory, molecular graphs, and absolute reaction rates. Information topological indices of molecular graphs were used as generalized structural characteristics of molecules. They are a quantitative measure of the structural complexity of molecules and are expressed in information units. The gas-phase process of fragmentation of molecules under electron impact was used as a general reaction series for all volatiles. In terms of information theory, the mass spectrum represents the distribution of probabilities of the formation of ions of each type, and the information entropy of this distribution appears to be an integral characteristic of the reactivity of a molecule during fragmentation under electron impact in the gas phase. Using organic and organometallic compounds of several classes (ferrocene derivatives, arylsilanes, aromatic azo compounds,etc.) as examples, linear correlations between the information indices of the mass spectra and the information topological indices of the appropriate molecular graphs or electronic parameters of molecules have been found, which testifies that the approach suggested is adequate.Translated fromIzvestiya Akodemii Nouk. Seriya Khimicheskaya, No. 11, pp. 2683–2688, November, 1996.     

Stepwise bromination of two acetylene molecules on a butterfly-type tetrairon core and reactivity of the resulting bromoacetylene fragment toward nucleophiles

Treatment of the acetylene-coordinated tetrairon cluster, [(eta5-C5H4Me)4Fe4(HCCH)2]+, with N-bromosuccinimide led to stepwise bromination of two acetylene ligands to form [(eta5-C5H4Me)4Fe4(HCCBr)(HCCH)]+, [(eta5-C5H4Me)4Fe4(HCCBr)2]+, [(eta5-C5H4Me)4Fe4(BrCCBr)(HCCBr)]+, and [(eta5-C5H4Me)4Fe4(BrCCBr)2]+. The reactivity of the bromoacetylene fragment in [(eta5-C5H4Me)4Fe4(HCCBr)(HCCH)]+ toward water, pyridine, and ZnMe2 was also investigated.     

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals.

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.